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Wed 11 Jan - Thu 12 Jan 2023
09:30 - 13:00

Venue: Bioinformatics Training Facility - Online LIVE Training

Provided by: Bioinformatics


Bookings cannot be made on this event (Event is completed).

Other dates:

Tue 23 Jan 2024

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EMBL-EBI: Network Analysis with Cytoscape (Online)

Wed 11 Jan - Thu 12 Jan 2023


This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • This workshop is aimed at researchers interested in proteins, network analysis, protein-protein interactions and related areas
  • Biologists and bioinformaticians
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

No prior experience required


Number of sessions: 2

# Date Time Venue Trainers
1 Wed 11 Jan   09:30 - 13:00 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training Kalpana Paneerselvam,  Eliot Ragueneau,  Juanjo Medina
2 Thu 12 Jan   09:30 - 13:00 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training Kalpana Paneerselvam,  Eliot Ragueneau,  Juanjo Medina
Topics covered

Bioinformatics, Pathway or network analysis, Pathway or network visualisation


After this course you should be able to:

  • Utilise a range of Cytoscape apps to generate and analyse interaction networks
  • Use different analysis apps within Cytoscape: IntAct, MCODE, ClueGO
  • Import your data into Cytoscape
  • Perform network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials

During this course you will learn about:

  • Biological network representation and analysis
  • Protein-protein interactions and PPI databases introduction
  • Basic Cytoscape functionality and use of apps for access to molecular interaction data (IntAct), clustering (MCODE) and GO enrichment analysis (ClueGO)

Presentations and demonstrations


This is subject to change in line with the online training schedule.

Day 1 Topics
Session 1 Introduction: Network analysis basics, Molecular interactions and interaction databases: IntAct and Cytoscape

Comfort Break
Session 2 Cytoscape practical: Accessing interaction data through the IntAct app

Session 3 Q&A session

Day 2 Topics
Session 1 Cytoscape practical: Data integration in Cytoscape

Session 2 Cytoscape practical: Topological analysis in Cytoscape: clustering with MCODE
Comfort Break
Session 3 Cytoscape practical: Enrichment analysis in Cytoscape: ClueGO
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

Two half day sessions


Once per year


Related courses
Specialised Research Topics

Booking / availability